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Marine microbial diversity

Guillem Salazar, Shinichi Sunagawa
2017 Current Biology  
doi:10.1016/j.cub.2017.01.017 pmid:28586685 fatcat:yuztdbzlnbfa5cjfuevrsz5evm

Threatened Corals Provide Underexplored Microbial Habitats

Shinichi Sunagawa, Cheryl M. Woodley, Mónica Medina, Stuart A. Sandin
2010 PLoS ONE  
Sunagawa in partial fulfillment of his doctoral dissertation in Quantitative and Systems Biology at UC Merced. This is contribution #3 of the STRI Caribbean Reef Futures initiative.  ... 
doi:10.1371/journal.pone.0009554 pmid:20221265 pmcid:PMC2832684 fatcat:bkat43r7i5dabdwi7v4cco2flu

A roadmap for metagenomic enzyme discovery

Serina L. Robinson, Jörn Piel, Shinichi Sunagawa
2021 Natural product reports (Print)  
Sunagawa studied Biochemistry and Marine Ecology in Germany, and obtained his PhD in 2010 at the University of California, Merced, USA.  ...  essentially every sampling location conceivable, including the hindguts of termites, 7 cheese rinds, 8 and the International Space Station. 9 Enabled by next-generation sequencing technologies, Shinichi  ... 
doi:10.1039/d1np00006c pmid:34821235 pmcid:PMC8597712 fatcat:43y3eqguw5ex5ikz7ihs7r3lg4

Highly purified natural rubber. III. Biological properties

Masaharu HAYASHI, Shinichi NAKADE, Makoto SUNAGAWA, Teturo KANO, Kumiko TSUKAMOTO, Yasuyuki TANAKA
Highly deproteinized natural rubber (HDPNR) latex was prepared by incubation of highammonia latex (HA-latex) with proteolytic enzyme in the presence of surfactant (s) followed by concentration with centrifuge. The nitrogen content of HDPNR was less than 0.02%. The potential of Type I allergy was evaluated by passive cutaneous anaphylaxis reaction test (PCA tests) and Enzyme-linked immunosorbent assay (ELISA). Antibody was not detected in the serum of animals sensitized with HDPNR latex by these two test. (
doi:10.2324/gomu.69.562 fatcat:jsfhwxocmnf5flr2ncdcbgd4ky

Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)

Joseph Heras, Kelly McClintock, Shinichi Sunagawa, Andres Aguilar
2015 BMC Genomics  
The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine
more » ... shes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates. Results: We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions. Conclusions: We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.
doi:10.1186/s12864-015-1870-0 pmid:26329285 pmcid:PMC4557894 fatcat:m43wcabumnhuzn5nsjyzqrqs5i

RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense

Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi Sunagawa
2017 Frontiers in Microbiology  
The less abundant species were not easily detected (Sunagawa et al., 2013) .  ...  Thus, in the oceans, it appears that RNase H-like proteins represent (Sunagawa et al., 2015) .  ... 
doi:10.3389/fmicb.2017.01745 pmid:28959243 pmcid:PMC5603734 fatcat:q2z2hg64ffbwtipsq5ynh2m5tu

metaSNV: A tool for metagenomic strain level analysis

Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork, Kai Wang
2017 PLoS ONE  
Formal analysis : analysis Robin Munch, Shinichi Sunagawa. Funding acquisition: Peer Bork. Investigation: Paul Igor Costea.  ...  Methodology: Paul Igor Costea, Robin Munch, Lucas Paoli, Shinichi Sunagawa. Table 1 . 1 Resource comparison for metaSNV and MIDAS.  ... 
doi:10.1371/journal.pone.0182392 pmid:28753663 pmcid:PMC5533426 fatcat:yb6csw2us5av5isfapfan7nnna

Inter-individual differences in the gene content of human gut bacterial species

Ana Zhu, Shinichi Sunagawa, Daniel R Mende, Peer Bork
2015 Genome Biology  
Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial
more » ... strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. Results: A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. Conclusion: Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.
doi:10.1186/s13059-015-0646-9 pmid:25896518 pmcid:PMC4428241 fatcat:yyxqt76os5gavgjmjmx777xkkm

Metagenomic insights into the human gut resistome and the forces that shape it

Kristoffer Forslund, Shinichi Sunagawa, Luis P. Coelho, Peer Bork
2014 Bioessays  
The human gut is populated by a vast number of bacteria, which play a critical role in human health. In recent years, attention has focused on the gut bacteria as a reservoir of antibiotic resistance genes (ARGs). Both culture-dependent and culture-independent methods have been applied to investigate numerous ARGs, collectively called the antibiotic resistome, harbored by gut bacteria. This has led to an increased understanding of the overall profile of the gut antibiotic resistome, although it
more » ... remains incompletely understood. In this review, we summarize the recent research findings on the human gut antibiotic resistome, with an emphasis on progress achieved using the culture-independent metagenomic strategy. We also describe the features of different available ARG databases used for annotation in metagenomic analysis, discuss the potential problems and limitations in current research, and suggest several directions for future investigation.
doi:10.1002/bies.201300143 pmid:24474281 fatcat:fnn5gjvd3vc6dd2v53mkisfelq

Temporal and technical variability of human gut metagenomes

Anita Y Voigt, Paul I Costea, Jens Roat Kultima, Simone S Li, Georg Zeller, Shinichi Sunagawa, Peer Bork
2015 Genome Biology  
Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced
more » ... tion, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject. Results: We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods. Conclusions: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.
doi:10.1186/s13059-015-0639-8 pmid:25888008 pmcid:PMC4416267 fatcat:mksqwxxgezhrblg7jchblhapbe

The Ocean Gene Atlas: exploring the biogeography of plankton genes online [article]

Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Aurelien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp
2018 biorxiv/medrxiv   pre-print
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for homology and displaying the abundances of genes in the context of environmental features
more » ... emperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences, and ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes, both produced by the Tara Oceans sequencing effort. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at:
doi:10.1101/271882 fatcat:fduxszsqnna5fmnrnyhkwzcqqu

SIAMCAT: user-friendly and versatile machine learning workflows for statistically rigorous microbiome analyses [article]

Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller
2020 bioRxiv   pre-print
We thank members of the Zeller, Sunagawa and Bork group for fruitful discussions and the EMBL Information Technology Core Facility for support with high-performance computing.  ... 
doi:10.1101/2020.02.06.931808 fatcat:jraubeuycrbt5chykvybdlzzuy

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes

Guillem Salazar, Hans-Joachim Ruscheweyh, Falk Hildebrand, Silvia G Acinas, Shinichi Sunagawa, Yann Ponty
2021 Bioinformatics  
The authors also acknowledge the constructive input from members of the Sunagawa Lab and von Mering group as well as the ETH Zürich High Performance Computing facilities for computational support.  ... 
doi:10.1093/bioinformatics/btab465 pmid:34260698 pmcid:PMC8696115 fatcat:2j7aqfnpmrhavcxxscwtcywcoa

Global genetic capacity for mixotrophy in marine picocyanobacteria

Alexis P Yelton, Silvia G Acinas, Shinichi Sunagawa, Peer Bork, Carlos Pedrós-Alió, Sallie W Chisholm
2016 The ISME Journal  
., 2011; Sunagawa et al., 2015) .  ...  Sample collection and preparation were described previously (Logares et al., 2014; Pesant et al., 2015; Sunagawa et al., 2015) .  ... 
doi:10.1038/ismej.2016.64 pmid:27137127 pmcid:PMC5148188 fatcat:7ojv4egrdvb4lpkkhdf3g6w6lq

The impact of RTN on performance fluctuation in CMOS logic circuits

Kyosuke Ito, Takashi Matsumoto, Shinichi Nishizawa, Hiroki Sunagawa, Kazutoshi Kobayashi, Hidetoshi Onodera
2011 2011 International Reliability Physics Symposium  
In this paper, the impact of Random Telegraph Noise (RTN) on CMOS logic circuits observed in a Circuit Matrix Array is reported. We discuss the behavior of RTN under circuit operation, and reveal that the impact of RTN, which is much smaller than that of within-die variation in a 65nm process, can have a severe effect on the performance of a sequential logic gate under low voltage operation.
doi:10.1109/irps.2011.5784563 fatcat:actko5bitzd5lk34taerrghkpe
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